Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A11 F1 I1 R1 757 76.1 3598070 93.4% 3360597 108.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,260,528 A→G I92I (ATT→ATC)  dauA ← C4‑dicarboxylic acid transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,260,5280AG96.2% 177.5 / ‑0.5 52coding (276/1680 nt)dauAC4‑dicarboxylic acid transporter
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (26/24);  minor base . (1/1);  total (27/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.57e-01

AGGTGACGGAAACCGGAATATACTCAATCAGGCGACCAAAGCGTGCCAGACCCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGAATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCGGT‑ATATAAACCGTACTGGGGTGCCACACCACTACCAATAGCCAA  >  NC_000913/1260395‑1260656
                                                                                                                                     |                                                                                                                                 
aGGTGACGGAAACCGGAATATACTCAATCAGGCGACCAAAGCGTGCCAGACCCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTAc                                                                                                                              <  2:1671852/139‑1 (MQ=255)
   tGACGGAAACCGGAATATACTCAATCAGGCGACCAAAGCGTGCCAGACCCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACcac                                                                                                                           >  1:994887/1‑139 (MQ=255)
      cGGAAACCGGAATATACTCACTCAGGCGACCAAAGCGTGCCAGACCCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACcacata                                                                                                                        >  1:1056793/1‑137 (MQ=255)
                              ggCGACCAAAGCGTGCCAGACTCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCt                                                                                                <  2:1056793/139‑1 (MQ=255)
                              ggCGACCAAAGCGTGCCAGACCCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCt                                                                                                >  2:1706224/1‑139 (MQ=255)
                                cGACCAAAGCGTGCCAGACCCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCgg                                                                                                       <  2:1729597/130‑1 (MQ=255)
                                cGACCAAAGCGTGCCAGACCCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCgg                                                                                                       >  1:1729597/1‑130 (MQ=255)
                                   ccAAAGCGTGCCAGACCCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCATTCGGACCGGAAACGCTAAAGc                                                                                           >  2:1057485/1‑139 (MQ=255)
                                   ccAAAGCGTGCCAGACCCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGc                                                                                           >  1:1117583/1‑139 (MQ=255)
                                         cGTGCCAGACCCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGacc                                                                                     <  1:1172196/139‑1 (MQ=255)
                                         cGTGCCAGACCCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAG‑G‑ATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGaccca                                                                                   >  2:126482/1‑139 (MQ=255)
                                           tGCCAGACCCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGaccca                                                                                   <  2:1363472/139‑1 (MQ=255)
                                           tGCCAGACCCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGaccca                                                                                   <  2:1495352/139‑1 (MQ=255)
                                                 aCCCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTc                                                                             >  2:1540810/1‑139 (MQ=255)
                                                               aaaaGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAAt                                                               >  1:1541016/1‑139 (MQ=255)
                                                                    aTCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCg                                                          >  2:354219/1‑139 (MQ=255)
                                                                    aTCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCg                                                          >  2:438149/1‑139 (MQ=255)
                                                                      ccccGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGcc                                                                                                                    >  2:1259590/1‑79 (MQ=255)
                                                                      ccccGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGcc                                                                                                                    <  1:1259590/79‑1 (MQ=255)
                                                                       cccGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCaa                                                       >  1:596856/1‑139 (MQ=255)
                                                                            cAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAG‑G‑ATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGc                                                <  1:126482/139‑1 (MQ=255)
                                                                              gCAAGGTCGTAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATTACAATCCCCGCAACAGCTGc                                                <  1:1057485/139‑1 (MQ=255)
                                                                              gCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGc                                                <  1:438149/139‑1 (MQ=255)
                                                                               cAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGt                                                                                                               >  1:793936/1‑75 (MQ=255)
                                                                               cAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGt                                                                                                               <  2:793936/75‑1 (MQ=255)
                                                                               cAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCg                                               >  1:623914/1‑139 (MQ=255)
                                                                               cAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCg                                               <  1:1706224/139‑1 (MQ=255)
                                                                                 aGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCGGt                                             <  1:874476/139‑1 (MQ=255)
                                                                                 aGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCGGt                                             >  2:874476/1‑139 (MQ=255)
                                                                                 aGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCGGt                                             >  1:1666544/1‑139 (MQ=255)
                                                                                      gCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCGGt‑atata                                       <  2:1004148/139‑1 (MQ=255)
                                                                                       cAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCg                                               >  1:439940/1‑131 (MQ=255)
                                                                                       cAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCg                                               <  2:439940/131‑1 (MQ=255)
                                                                                            agcagTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCt                                                                                                <  1:794124/77‑1 (MQ=255)
                                                                                            agcagTCCTGCCAGTCCAAACTGTTGCAACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCt                                                                                                >  2:794124/1‑77 (MQ=255)
                                                                                             gcagTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGt                                                                              >  2:1294150/1‑94 (MQ=255)
                                                                                             gcagTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGt                                                                              <  1:1294150/94‑1 (MQ=255)
                                                                                                gTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCGGT‑ATATAAACCGTACTg                             <  2:960251/139‑1 (MQ=255)
                                                                                                       cAGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCGGT‑ATATAAACCGTACTGGGGTGcc                      <  1:215655/139‑1 (MQ=255)
                                                                                                        aGTCCAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCGGT‑ATATAAACCGTACTGGGGTGCca                     >  2:1593861/1‑139 (MQ=255)
                                                                                                           ccAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGc                                                                        <  1:1372032/86‑1 (MQ=255)
                                                                                                           ccAAACTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGc                                                                        >  2:1372032/1‑86 (MQ=255)
                                                                                                             aaaCTGTTGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCGGT‑ATATAAACCGTACTGGGGTGCCAcacca                <  1:1540810/139‑1 (MQ=255)
                                                                                                                    tGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCGGTAATATAAACCGTACTGGGGTGCca                     >  2:1723194/1‑128 (MQ=255)
                                                                                                                    tGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCGGTAATATAAACCGTACTGGGGTGCca                     <  1:1723194/128‑1 (MQ=255)
                                                                                                                    tGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCGGT‑ATATAAACCGTACTGGGGTGCCACACCACTACCaa         <  1:354219/139‑1 (MQ=255)
                                                                                                                    tGCGACACGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCGGT‑ATATAAACCGTACTGGGGTGCCACACCACTACCaa         >  1:645421/1‑139 (MQ=255)
                                                                                                                    tGCGACACGGGATAGAGGATTACCACAAATACCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGt                                                                              >  2:229018/1‑71 (MQ=255)
                                                                                                                    tGCGACACGGGATAGAGGATTACCACAAATACCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGt                                                                              <  1:229018/71‑1 (MQ=255)
                                                                                                                        acacGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGaccc                                                                                    <  1:1700985/61‑1 (MQ=255)
                                                                                                                        acacGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGaccc                                                                                    >  2:1700985/1‑61 (MQ=255)
                                                                                                                           cGGGATAGAGGATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCGGT‑ATATAAACCGTACTGGGGTGCCACACCACTACCAATAGCCaa  >  2:169225/1‑139 (MQ=255)
                                                                                                                                     |                                                                                                                                 
AGGTGACGGAAACCGGAATATACTCAATCAGGCGACCAAAGCGTGCCAGACCCATCAGAATCAAAAAGATCCCCGACAGCAAGGTCGCAACCAGCAGTCCTGCCAGTCCAAACTGTTGCGACACGGGATAGAGAATTACCACAAATGCCGCAGTCGGACCGGAAACGCTAAAGCGTGACCCACCCGTCAGAGCAATGACAATCCCCGCAACAGCTGCGGT‑ATATAAACCGTACTGGGGTGCCACACCACTACCAATAGCCAA  >  NC_000913/1260395‑1260656

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A